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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ), 'gf_id' => 'HOM05D001369', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001369' ), 'data_identifier' => 'HOM05D001369', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001369', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06220' => 'bna', 'A03p10040' => 'bna', 'A03p27010' => 'bna', 'A03p61230' => 'bna', 'A06p09530' => 'bna', 'A09p55720' => 'bna', 'Aa31LG1G14300' => 'aar', 'Aa31LG1G2720' => 'aar', 'Aa31LG2G100' => 'aar', 'Aa31LG2G17880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2056' => 'aag', 'Actinidia11874' => 'ach', 'Actinidia13218' => 'ach', 'Actinidia21926' => 'ach', 'Actinidia22320' => 'ach', 'Actinidia26724' => 'ach', 'Actinidia26725' => 'ach', 'Actinidia26879' => 'ach', 'Actinidia39263' => 'ach', 'Ah.09g224110' => 'amhyb', 'Ah.09g234430' => 'amhyb', 'Ah.09g234440' => 'amhyb', 'Ah.16g104760' => 'amhyb', 'AL2G13500' => 'aly', 'AL4G16620' => 'aly', 'AL6G31920' => 'aly', 'AL7G19820' => 'aly', 'Aqoxy1G02906' => 'aox', 'Aqoxy3G02577' => 'aox', 'Aqoxy4G02233' => 'aox', 'Aqoxy7G02458' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4XP552' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6P9NVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.798C6B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C2ZAQ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LDS5WE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7SKGD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MQIQ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRQS70' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RUN5KQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFEI8X' => 'arhy', 'AT1G62390' => 'ath', 'AT2G25290' => 'ath', 'AT4G32070' => 'ath', 'AT5G20360' => 'ath', 'ATR0624G073' => 'atr', 'ATR0743G253' => 'atr', 'ATR1152G020' => 'atr', 'ATR1152G021' => 'atr', 'Atru.chr10.2314' => 'acertr', 'Atru.chr7.2013' => 'acertr', 'Atru.chr7.2481' => 'acertr', 'AUR62011225' => 'cqu', 'AUR62012435' => 'cqu', 'AUR62012766' => 'cqu', 'AUR62020009' => 'cqu', 'AUR62021891' => 'cqu', 'AUR62031559' => 'cqu', 'BcaB01g03004' => 'bca', 'BcaB01g04790' => 'bca', 'BcaB08g35173' => 'bca', 'BcaB08g36496' => 'bca', 'BcaC07g40873' => 'bca', 'BcaC07g40874' => 'bca', 'BcaC09g51997' => 'bca', 'BcaNung03136' => 'bca', 'BolC1t00683H' => 'bol', 'BolC3t13630H' => 'bol', 'BolC3t15583H' => 'bol', 'BolC5t29873H' => 'bol', 'BolC7t46356H' => 'bol', 'BolC8t51442H' => 'bol', 'BraA01t00589Z' => 'bra', 'BraA03t10314Z' => 'bra', 'BraA03t11912Z' => 'bra', 'BraA03t15167Z' => 'bra', 'BraA06t24143Z' => 'bra', 'BraA09t40973Z' => 'bra', 'C01p06860' => 'bna', 'C03p11580' => 'bna', 'C03p32420' => 'bna', 'C05p11250' => 'bna', 'C07p59080' => 'bna', 'C08p38720' => 'bna', 'CAN.G1014.56' => 'can', 'CAN.G123.6' => 'can', 'CAN.G1281.5' => 'can', 'CAN.G1461.3' => 'can', 'CAN.G1475.4' => 'can', 'CANSAT11G0468' => 'cansat', 'CANSAT25G3725' => 'cansat', 'CARHR012360' => 'chi', 'CARHR116250' => 'chi', 'CARHR192480' => 'chi', 'CARHR239980' => 'chi', 'Carub.0002s0259' => 'cru', 'Carub.0004s0491' => 'cru', 'Carub.0006s1875' => 'cru', 'Carub.0007s0848' => 'cru', 'Ca_00706_v3' => 'car', 'Ca_03105_v3' => 'car', 'Ca_13037_v3' => 'car', 'Ca_21056_v3' => 'car', 'Ca_21636_v3' => 'car', 'Ca_30357_v3' => 'car', 'CBR_g34700' => 'cbr', 'Cc06_g07650' => 'ccan', 'Cc08_g00330' => 'ccan', 'Cc09_g01100' => 'ccan', 'CDE02G0147' => 'cde', 'CDE04G3521' => 'cde', 'CDE05G1259' => 'cde', 'CDE05G2449' => 'cde', 'CDE05G3238' => 'cde', 'CDE05G3626' => 'cde', 'CDE11G1020' => 'cde', 'Cfa000137' => 'cfa', 'Cfa013116' => 'cfa', 'Ciclev10007597m.g' => 'ccl', 'Ciclev10007599m.g' => 'ccl', 'Ciclev10014348m.g' => 'ccl', 'CiPaw.03G252500' => 'cil', 'CiPaw.08G009100' => 'cil', 'CiPaw.09G099800' => 'cil', 'CiPaw.10G075600' => 'cil', 'ClCG01G009820' => 'cla', 'ClCG05G016630' => 'cla', 'ClCG06G011870' => 'cla', 'COL.COLO4_18898' => 'col', 'COL.COLO4_33366' => 'col', 'Cpa.g.sc152.59' => 'cpa', 'Cpa.g.sc187.12' => 'cpa', 'Cpa.g.sc46.68' => 'cpa', 'Cre10.g430501' => 'cre', 'CsaV3_1G028330' => 'csa', 'CsaV3_1G045950' => 'csa', 'CsaV3_4G036920' => 'csa', 'CSS0003786' => 'camsi', 'CSS0012374' => 'camsi', 'CSS0038189' => 'camsi', 'CSS0041103' => 'camsi', 'CSS0041466' => 'camsi', 'DCAR_002208' => 'dca', 'DCAR_003107' => 'dca', 'DCAR_009344' => 'dca', 'DCAR_017771' => 'dca', 'DCAR_023687' => 'dca', 'DCAR_027852' => 'dca', 'Dinv13950' => 'din', 'Dinv15872' => 'din', 'Dinv20116' => 'din', 'Dinv36448' => 'din', 'Duzib168G0614' => 'dzi', 'Duzib170G1077' => 'dzi', 'Duzib187G0833' => 'dzi', 'Duzib213G0148' => 'dzi', 'ECA233G1302' => 'eca', 'ECA236G3841' => 'eca', 'ECA240G4788' => 'eca', 'ECA246G0810' => 'eca', 'ECA247G2724' => 'eca', 'ECA248G0718' => 'eca', 'EL10Ac2g04166' => 'bvu', 'EL10Ac8g18784' => 'bvu', 'EL10Ac8g20143' => 'bvu', 'Eucgr.C00325' => 'egr', 'Eucgr.C00481' => 'egr', 'Eucgr.C00483' => 'egr', 'Eucgr.C02736' => 'egr', 'Eucgr.D01369' => 'egr', 'Eucgr.D01375' => 'egr', 'FAN19G1069' => 'fan', 'FAN19G1635' => 'fan', 'FAN20G2041' => 'fan', 'FAN21G0839' => 'fan', 'FAN23G0070' => 'fan', 'FAN24G1381' => 'fan', 'FAN25G1688' => 'fan', 'FAN26G2010' => 'fan', 'FAN27G0110' => 'fan', 'FvH4_1g02010' => 'fve', 'FvH4_2g28600' => 'fve', 'FvH4_3g01270' => 'fve', 'Glyma.04G064900' => 'gma', 'Glyma.06G066100' => 'gma', 'Glyma.07G264300' => 'gma', 'Glyma.09G091200' => 'gma', 'Glyma.13G163600' => 'gma', 'Glyma.17G009700' => 'gma', 'Glyma.17G107300' => 'gma', 'Glyma.17G213466' => 'gma', 'Glyma.17G213532' => 'gma', 'Gohir.A01G094700' => 'ghi', 'Gohir.A05G056350' => 'ghi', 'Gohir.A05G056575' => 'ghi', 'Gohir.A08G090400' => 'ghi', 'Gohir.A13G130170' => 'ghi', 'Gohir.A13G180900' => 'ghi', 'Gohir.A13G201900' => 'ghi', 'Gohir.D01G079200' => 'ghi', 'Gohir.D05G058800' => 'ghi', 'Gohir.D08G101400' => 'ghi', 'Gohir.D13G133400' => 'ghi', 'Gohir.D13G188700' => 'ghi', 'Gohir.D13G207700' => 'ghi', 'Gorai.002G103800' => 'gra', 'Gorai.004G109400' => 'gra', 'Gorai.009G059900' => 'gra', 'Gorai.013G149700' => 'gra', 'Gorai.013G214100' => 'gra', 'Gorai.013G236600' => 'gra', 'GSVIVG01004881001' => 'vvi', 'GSVIVG01007268001' => 'vvi', 'GSVIVG01012858001' => 'vvi', 'GSVIVG01035938001' => 'vvi', 'HanXRQChr01g0006551' => 'han', 'HanXRQChr01g0017001' => 'han', 'HanXRQChr03g0089651' => 'han', 'HanXRQChr05g0133291' => 'han', 'HanXRQChr05g0143451' => 'han', 'HanXRQChr09g0241851' => 'han', 'HanXRQChr13g0403221' => 'han', 'HanXRQChr16g0511381' => 'han', 'Haze_06887' => 'cav', 'Haze_21480' => 'cav', 'Haze_25445' => 'cav', 'Hma1.2p1_0298F.1_g117380' => 'hma', 'Hma1.2p1_1816F.1_g303960' => 'hma', 'HPP92_001210' => 'vpl', 'HPP92_012756' => 'vpl', 'HPP92_019926' => 'vpl', 'Hund04437' => 'sun', 'Hund21594' => 'sun', 'Lalb_Chr08g0233571' => 'lal', 'Lalb_Chr08g0244241' => 'lal', 'Lalb_Chr12g0198411' => 'lal', 'Lalb_Chr13g0301321' => 'lal', 'Lalb_Chr15g0087851' => 'lal', 'Lalb_Chr18g0056841' => 'lal', 'Lalb_Chr20g0119151' => 'lal', 'Lalb_Chr24g0402101' => 'lal', 'Lj1P1237T32' => 'lonja', 'Lj1P1237T36' => 'lonja', 'Lj2P263T25' => 'lonja', 'Lj4g0001127' => 'lja', 'Lj4g0003401' => 'lja', 'Lj5g0022242' => 'lja', 'Lj6g0004666' => 'lja', 'Lj7C439T1' => 'lonja', 'Lj8A726T44' => 'lonja', 'Lj9A704T73' => 'lonja', 'Lsat_1_v5_gn_3_86861' => 'lsa', 'Lsat_1_v5_gn_3_9221' => 'lsa', 'Lsat_1_v5_gn_4_122861' => 'lsa', 'Lsat_1_v5_gn_5_1660' => 'lsa', 'Lsat_1_v5_gn_6_115720' => 'lsa', 'Lsat_1_v5_gn_6_20341' => 'lsa', 'Lsat_1_v5_gn_7_45820' => 'lsa', 'Lsat_1_v5_gn_8_62941' => 'lsa', 'Manes.06G044100' => 'mes', 'Manes.14G119500' => 'mes', 'Manes.16G125100' => 'mes', 'Manes.17G024482' => 'mes', 'Mapoly0099s0038' => 'mpo', 'MBI14_g24236_MAGBIO' => 'mbi', 'MBI15_g25761_MAGBIO' => 'mbi', 'MBI16_g13189_MAGBIO' => 'mbi', 'MCO04G299' => 'mco', 'MCO06G030' => 'mco', 'MD02G1018300' => 'mdo', 'MD05G1354100' => 'mdo', 'MD08G1152700' => 'mdo', 'MD10G1328200' => 'mdo', 'MD15G1129300' => 'mdo', 'MD15G1162300' => 'mdo', 'Medtr1g012840' => 'mtr', 'Medtr2g025130' => 'mtr', 'Medtr2g451540' => 'mtr', 'Medtr4g132780' => 'mtr', 'MELO3C010279.2' => 'cme', 'MELO3C016991.2' => 'cme', 'MELO3C021716.2' => 'cme', 'Migut.A00015' => 'egut', 'Migut.H01596' => 'egut', 'Migut.J01237' => 'egut', 'Migut.K00398' => 'egut', 'MSTRG.13125' => 'ama', 'MSTRG.26022' => 'ama', 'MSTRG.26325' => 'ama', 'MSTRG.6076' => 'ama', 'Nitab4.5_0000005g0080' => 'nta', 'Nitab4.5_0000857g0100' => 'nta', 'Nitab4.5_0001793g0120' => 'nta', 'Nitab4.5_0002286g0030' => 'nta', 'Nitab4.5_0002845g0040' => 'nta', 'Nitab4.5_0004694g0030' => 'nta', 'Nitab4.5_0004821g0010' => 'nta', 'Nitab4.5_0007718g0030' => 'nta', 'Nitab4.5_0008174g0010' => 'nta', 'Nitab4.5_0010174g0010' => 'nta', 'Nitab4.5_0012888g0010' => 'nta', 'Nitab4.5_0015929g0010' => 'nta', 'Nn1g03371' => 'nnu', 'Nn1g07305' => 'nnu', 'Nn2g12193' => 'nnu', 'Nn4g25153' => 'nnu', 'Nn8g39648' => 'nnu', 'Oeu003162.1' => 'oeu', 'Oeu007159.1' => 'oeu', 'Oeu012277.1' => 'oeu', 'Oeu027836.1' => 'oeu', 'Oeu036867.1' => 'oeu', 'Oeu049714.1' => 'oeu', 'Oeu051710.3' => 'oeu', 'Oeu051872.1' => 'oeu', 'Oeu051874.1' => 'oeu', 'Oeu052256.1' => 'oeu', 'Os08g0296900' => 'osa', 'Os09g0135400' => 'osa', 'Os09g0556200' => 'osa', 'Peaxi162Scf00088g00614' => 'pax', 'Peaxi162Scf00116g00131' => 'pax', 'Peaxi162Scf00294g00082' => 'pax', 'Peaxi162Scf00643g00009' => 'pax', 'Peaxi162Scf01096g00033' => 'pax', 'PGR004G2550' => 'pgr', 'PGR044G1709' => 'pgr', 'PGR142G3215' => 'pgr', 'PGSC0003DMG400014835' => 'stu', 'PGSC0003DMG400016728' => 'stu', 'PGSC0003DMG400019104' => 'stu', 'PGSC0003DMG400021460' => 'stu', 'PGSC0003DMG400026101' => 'stu', 'PGSC0003DMG400030723' => 'stu', 'Phvul.001G049601' => 'pvu', 'Phvul.003G082400' => 'pvu', 'Phvul.003G172500' => 'pvu', 'Phvul.009G091100' => 'pvu', 'Phvul.009G212300' => 'pvu', 'Potri.004G002900' => 'ptr', 'Potri.006G258300' => 'ptr', 'Potri.011G021000' => 'ptr', 'Potri.018G023500' => 'ptr', 'Potri.018G121100' => 'ptr', 'PRCOL_00001726' => 'pco', 'Prupe.1G484900' => 'ppe', 'Prupe.4G013700' => 'ppe', 'Prupe.7G257700' => 'ppe', 'Psat1g021000' => 'psa', 'Psat1g177480' => 'psa', 'Psat4g003160' => 'psa', 'Psat6g028080' => 'psa', 'PSO017G0060' => 'pso', 'PSO170G0882' => 'pso', 'PSO541G5015' => 'pso', 'PSO675G9360' => 'pso', 'QL02p020857' => 'qlo', 'QL02p090778' => 'qlo', 'QL03p008110' => 'qlo', 'QL05p070150' => 'qlo', 'RcHm_v2.0_Chr2g0087071' => 'rch', 'RcHm_v2.0_Chr5g0001821' => 'rch', 'RcHm_v2.0_Chr6g0297371' => 'rch', 'Rhsim02G0104800' => 'rsi', 'Rhsim02G0205000' => 'rsi', 'Rhsim03G0253200' => 'rsi', 'Rhsim13G0149100' => 'rsi', 'Sabra04G0001500' => 'sbr', 'Sabra06G0044300' => 'sbr', 'Sabra11G0011100' => 'sbr', 'Sabra11G0012900' => 'sbr', 'Sabra18G0026000' => 'sbr', 'Sabra18G0099800' => 'sbr', 'Sabra18G0101600' => 'sbr', 'SalBow1G0472' => 'sbo', 'SalBow1G5414' => 'sbo', 'SalBow1G6526' => 'sbo', 'SalBow4G2817' => 'sbo', 'Sc17g0007620' => 'sci', 'Sc18g0000120' => 'sci', 'Sc23g0006610' => 'sci', 'Sed0006382' => 'sed', 'Sed0012889' => 'sed', 'Sed0016854' => 'sed', 'SEGI_09463' => 'sgi', 'SEGI_20115' => 'sgi', 'SEGI_23476' => 'sgi', 'SGA_v2.0_scaffold20G09088' => 'sas', 'SGA_v2.0_scaffold504G52523' => 'sas', 'SGA_v2.0_scaffold64G21972' => 'sas', 'SGA_v2.0_scaffold89G27490' => 'sas', 'Solyc02g036360.1' => 'sly', 'Solyc02g081200.1' => 'sly', 'Solyc06g065910.3' => 'sly', 'Solyc07g007390.3' => 'sly', 'Solyc08g029190.3' => 'sly', 'Sopen02g011730' => 'spe', 'Sopen02g025840' => 'spe', 'Sopen06g024380' => 'spe', 'Sopen07g003460' => 'spe', 'Sopen08g010090' => 'spe', 'Sp2g02220' => 'spa', 'Sp4g04400' => 'spa', 'Sp6g24060' => 'spa', 'Sp7g29870' => 'spa', 'TAR020G0001' => 'tar', 'TAR170G0001' => 'tar', 'TAR383G0962' => 'tar', 'TAR626G1933' => 'tar', 'TAR629G3348' => 'tar', 'TAR677G0007' => 'tar', 'THA.LOC104798649' => 'tha', 'THA.LOC104803646' => 'tha', 'THA.LOC104811015' => 'tha', 'THA.LOC104815026' => 'tha', 'Thecc.07G005700' => 'tca', 'Thecc.09G020700' => 'tca', 'Thecc.09G137500' => 'tca', 'Thhalv10000057m.g' => 'esa', 'Thhalv10006907m.g' => 'esa', 'Thhalv10012833m.g' => 'esa', 'Thhalv10024479m.g' => 'esa', 'TPR.G11424' => 'tpr', 'TPR.G13131' => 'tpr', 'TPR.G14035' => 'tpr', 'TPR.G29432' => 'tpr', 'TPR.G37095' => 'tpr', 'TWI32G1288' => 'twi', 'TWI34G0741' => 'twi', 'TWI34G1629' => 'twi', 'TWI63G1289' => 'twi', 'TWI63G1338' => 'twi', 'TWI63G1734' => 'twi', 'unitig_0.g2708' => 'ugi', 'unitig_26.g9400' => 'ugi', 'unitig_32.g10882' => 'ugi', 'unitig_748.g7177' => 'ugi', 'unitig_748.g8270' => 'ugi', 'unitig_748.g8271' => 'ugi', 'unitig_749.g13620' => 'ugi', 'unitig_749.g13621' => 'ugi', 'vmacro06116' => 'vma', 'vmacro06118' => 'vma', 'vmacro11205' => 'vma', 'vmacro22981' => 'vma', 'vmacro23323' => 'vma', 'VMungo0459G0002' => 'vmu', 'VMungo0540G1139' => 'vmu', 'VMungo0647G1697' => 'vmu', 'VMungo1215G1812' => 'vmu', 'VMungo1309G1852' => 'vmu', 'VMungo1309G2638' => 'vmu', 'Zm00001eb125140' => 'zma', 'Zm00001eb285550' => 'zma', 'Zm00001eb307020' => 'zma', 'Zm00001eb320580' => 'zma', 'Zm00001eb414750' => 'zma' ) $gf_id = 'HOM05D001369' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001369' ) $data_identifier = 'HOM05D001369' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb414750' $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